Building robust transcriptomes with master splicing factors

Abstract

Coherent splicing networks arise from many discrete splicing decisions regulated in unison. Here, we examine the properties of robust, context-specific splicing networks. We propose that a subset of key splicing regulators, or "master splicing factors," respond to environmental cues to establish and maintain tissue transcriptomes during development.

Figure 1. Common motifs in splicing networks

A) Negative feedback of RNA binding proteins (RBPs) occurs when a splicing factor regulates a nonsense-mediated decay-coupled splicing event within its own transcript to repress its own protein expression and maintain steady state expression levels. B) Top panel: Positive feedback in splicing networks can occur through a double negative feedback loop. Double negative feedback results from the cross-regulation of two RBPs, producing two steady states each characterized by the exclusive expression of one of the RBPs. Bottom panel: Positive feedback also arises through composite feedback with a splicing factor (SF) and one or more transcription factors (TF) that results in a double positive feedback loop and bistability. In this case, either the SF and TF are both expressed, or the SF and TF are both off. Red hexagons indicate premature termination codons.

Figure 2. RNA binding protein cross-regulation in splicing networks

A) Model for the cross-regulation of an autoregulatory poison exon by Rbfox2. Binding of Rbfox2 inhibits inclusion of the poison exon (red hexagon indicates premature termination codon), leading to a higher steady-state expression level of the autoregulated protein in the presence of Rbfox2. B) Rbfox2 and Ptbp2 function in a splicing cascade during neuronal differentiation. Rbfox2 directly regulates a subset of targets involved in cytoskeletal organization. In addition, inhibition of autoregulatory splicing of Ptbp2 by Rbfox2 leads to Ptbp2 upregulation. Ptbp2, either in conjunction with Rbfox2 or independently, regulates the splicing of several genes involved in adherens junction formation. Together, these primary and secondary targets of Rbfox2 contribute to the specification of neural progenitor fate (Jangi et al., 2014; Licatalosi et al., 2012).

Figure 3. Bistability in Drosophila sex determination

The Drosophila sex determination pathway initiates a cascade of splicing events within RNA binding proteins and transcription factors that regulates sexual dimorphism. The master regulator Sxl drives the female-specific isoform of Tra, which generates female-specific isoforms of the transcription factors Dsx and Fru. Positive feedback loops are indicated as bold arrows. Red hexagon indicates premature termination codon.

Figure 4. Master splicing factors in myogenesis

Rbm24 and Rbm28 are master RNA binding proteins in skeletal muscle differentiation and maintenance. The master transcription factor MyoD activates Rbm24 and Rbm38 in skeletal muscle myoblasts, concurrent with E2f-dependent activation of cell proliferation and Rbm38 activation. In a negative feedback loop that counters E2f activity, Rbm24 and Rbm38 initiate exit from the cell cycle by stabilization of p21. Rbm24 drives differentiation through the stabilization of the critical myogenesis factor myogenin. Both Rbm24 and Rbm38 control muscle-dependent splicing in differentiated myotubes through the co-regulation of Rbfox1 target splicing events (Jin et al., 2010; Li et al., 2010; Miyamoto et al., 2009; Zhang et al., 2008). Bottom panel: Rbm24 acquires an active transcriptional superenhancer in skeletal muscle myoblasts (yellow and green circles) and retains the mark in differentiated myotubes, in which the Rbm38 superenhancer also becomes active (Hnisz et al., 2013).